8Y71 | pdb_00008y71

positive allosteric modulator(BMS986187)-bound delta-opioid receptor-Gi complex

• PDB DOI: https://doi.org/10.2210/pdb8Y71/pdb
• EM Map EMD-39009: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-02-03 Released: 2026-01-07 
• Deposition Author(s): Luo, P., Xu, Y., Wang, Y., Zhuang, Y., Xu, H.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure based design of a positive allosteric modulator of mu-opioid receptor for synergistic analgesia

Luo, P., Xu, Y., Wang, Y., Zhuang, Y., Xu, H.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 173.05 kDa 
• Atom Count: 8,933 
• Modeled Residue Count: 1,136 
• Deposited Residue Count: 1,564 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 2  Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	371	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	68	Bos taurus	Mutation(s): 0  Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212  Go to UniProtKB:  P63212

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	D [auth E]	248	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta-type opioid receptor	E [auth R]	523	Homo sapiens	Mutation(s): 0  Gene Names: OPRD1, OPRD
UniProt & NIH Common Fund Data Resources
Find proteins for P41143 (Homo sapiens) Explore P41143  Go to UniProtKB:  P41143
PHAROS:  P41143 GTEx:  ENSG00000116329

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D6B (Subject of Investigation/LOI)	F [auth R]	3,3,6,6-tetramethyl-9-[4-[(2-methylphenyl)methoxy]phenyl]-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione C31 H34 O4 UEKIYVKPQNKSDI-UHFFFAOYSA-N
A1D6F (Subject of Investigation/LOI)	G [auth R]	4-[(~{S})-[(2~{R},5~{S})-2,5-dimethyl-4-prop-2-enyl-piperazin-1-yl]-(3-methoxyphenyl)methyl]-~{N},~{N}-diethyl-benzamide C28 H39 N3 O2 KQWVAUSXZDRQPZ-XXAUWVGASA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-07 
Deposition Author(s): Luo, P., Xu, Y., Wang, Y., Zhuang, Y., Xu, H.E.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32130022
National Natural Science Foundation of China (NSFC)	China	82121005

Revision History  

• Version 1.0: 2026-01-07
  Type: Initial release